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1 <tool id="bcftools_annotate" name="BCFtools annotate" version="1.0.0">
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2 <description>Add or remove annotations</description>
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22
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3 <requirements>
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4 <requirement type="package" version="1.3">bcftools</requirement>
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5 </requirements>
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10
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6 <command>
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7 #if str( $input_file_index ) != "None":
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8 ln -s -f $input input_file.${input.ext} &&
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9 ln -s -f $input_file_index input_file.${input.ext}.tbi &&
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10 #end if
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11 #if str( $annotations_cond.set_annotations ) == "True":
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12 ln -s -f $annotations_cond.annotations annot_file.${annotations_cond.annotations.ext} &&
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13 ln -s -f $annotations_cond.annotations_index annot_file.${annotations_cond.annotations.ext}.tbi &&
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14 #end if
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15 bcftools annotate
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16 --output "${output_file}"
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17 --output-type "${output_type}"
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18 #if str( $regions_file ) != "None":
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19 --regions-file "${regions_file}"
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20 #end if
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21 #if str( $annotations_cond.set_annotations ) == "True":
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22 --annotations annot_file.${annotations_cond.annotations.ext}
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23 #if str( $annotations_cond.columns ) != "":
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24 --columns "${annotations_cond.columns}"
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25 #end if
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26 #if str( $annotations_cond.mark_sites_cond.set_mark_sites ) == "True":
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27 --mark-sites
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28 #if str( $annotations_cond.mark_sites_cond.present_or_absent ) == "present":
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29 "+${annotations_cond.mark_sites_cond.new_tag}"
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30 #else
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31 "-${annotations_cond.mark_sites_cond.new_tag}"
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32 #end if
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33 #end if
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34 #end if
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35 #if str( $regions ) != "":
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36 --regions "${regions}"
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37 #end if
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38 #if str( $samples_file ) != "None":
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39 --samples-file "${samples_file}"
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40 #end if
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41 #if str( $samples ) != "":
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42 --samples "${samples}"
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43 #end if
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44 #if str( $header_lines ) != "None":
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45 --header-lines "${header_lines}"
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46 #end if
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47 #if str( $expr_cond.set_expr ) == "True":
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48 #if str( $expr_cond.include_or_exclude ) == "include":
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49 --include "${expr_cond.expr}"
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50 #else
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51 --exclude "${expr_cond.expr}"
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52 #end if
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53 #end if
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54 #if str( $rename_chrs ) != "None":
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55 --rename-chrs "${rename_chrs}"
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56 #end if
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57 #if str( $remove ) != "":
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58 --remove "${remove}"
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59 #end if
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60
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61 #if str( $input_file_index ) != "None":
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62 input_file.${input.ext}
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63 #else
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64 $input
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65 #end if
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66 </command>
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67 <inputs>
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68 <param name="input" type="data" format="vcf,bcf,bgzip" label="VCF or BCF input file" help="Input file can optionally be compressed and indexed using Bgzip and Tabix Galaxy tools. In this case, select bgzipped file here and index below."/>
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69 <param name="input_file_index" type="data" optional="true" label="Input file index" help="Tabix-generated index for input file. Run Tabix Galaxy tool on bgzipped input file to create index."/>
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70 <param name="output_type" type="select" label="Output data type" help="-O">
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71 <option value="v" selected="true">VCF</option>
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72 <option value="b">BCF</option>
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73 </param>
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74 <conditional name="annotations_cond">
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75 <param name="set_annotations" type="boolean" checked="False" label="Set annotation file" help="-a, -c, -m"/>
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76 <when value="true">
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77 <param name="annotations" type="data" label="Compressed annotation file" help="-a. Bgzip-compressed VCF/ BED/ tab-delimited file with annotations. Run Bgzip Galaxy tool to compress annotation file."/>
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78 <param name="annotations_index" type="data" label="Compressed annotation file index" help="Tabix-generated index for annotation file. Run Tabix Galaxy tool on bgzipped annotation file to create index."/>
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79 <param name="columns" type="text" size="80" label="Annotation file columns" help="-c. Comma-separated list of columns or tags to carry over from the annotation file." />
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80
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81 <conditional name="mark_sites_cond">
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82 <param name="set_mark_sites" type="boolean" checked="False" label="Mark present/absent sites" help="-m. Annotate sites which are present or absent in the annotation file with a new INFO/TAG flag. Note: BCFtools has not implemented this yet for VCF files."/>
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83 <when value="true">
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84 <param name="present_or_absent" type="select" label="Mark present or absent sites">
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85 <option value="present">Present</option>
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86 <option value="absent">Absent</option>
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87 </param>
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88 <param name="new_tag" type="text" size="80" label="New INFO/TAG flag" />
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89 </when>
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90 </conditional>
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91
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92 </when>
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93 </conditional>
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94
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95 <param name="regions_file" type="data" optional="true" label="Regions file" help="-R. Regions specified in a VCF, BED, or tab-delimited file with columns CHROM, POS, and, optionally, POS_TO."/>
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96 <param name="regions" type="text" size="80" optional="True" label="Regions list" help="-r. Comma-separated list of regions. Format: chr|chr:pos|chr:from-to|chr:from-[,...]">
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97 <sanitizer invalid_char="">
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98 <valid initial="string.digits"><add value="CHRchr-:,"/> </valid>
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99 </sanitizer>
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100 </param>
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101 <param name="samples_file" type="data" optional="true" label="Samples file" help="-S. File of sample names to include. One sample per line."/>
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102 <param name="samples" type="text" size="80" optional="True" label="Samples list" help="-s. Comma-separated list of samples to include or exclude. (Excludes if prefixed with ^)" />
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103 <param name="header_lines" type="data" optional="true" label="Header lines" help="-h. File containing lines to append to VCF header."/>
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104 <conditional name="expr_cond">
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105 <param name="set_expr" type="boolean" checked="False" label="Filter by expression" help="-i, -e. Include/ exclude sites for which expression is true. Must use valid expression."/>
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106 <when value="true">
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107 <param name="include_or_exclude" type="select" label="Include or exclude by expression">
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108 <option value="include">Include</option>
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109 <option value="exclude">Exclude</option>
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110 </param>
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111 <param name="expr" type="text" size="80" label="Expression">
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112 <sanitizer invalid_char="">
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113 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid>
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114 </sanitizer>
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115 </param>
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116 </when>
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117 </conditional>
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118 <param name="rename_chrs" type="data" optional="true" label="Rename chromosomes" help="--rename-chrs. File containing chromosome renaming map, with "old_name new_name\n" pairs separated by whitespaces, each on a separate line."/>
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119 <param name="remove" type="text" size="80" label="List of annotations to remove" help="-x. Comma-separated list of annotations to remove." />
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120 </inputs>
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121 <outputs>
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122 <data name="output_file" format="vcf" label="${tool.name} on ${on_string}">
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123 <change_format>
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124 <when input="output_type" value="b" format="bcf" />
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125 </change_format>
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126 </data>
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127 </outputs>
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128 <help>
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129 **About this tool**
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130
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131 **BCFtools annotate**: Add or remove annotations.
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132
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133 Please see https://samtools.github.io/bcftools/bcftools.html for more info on options.
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134 </help>
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135 </tool>
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